Add aws batch profile

main.nf

@@ -60,7 +60,7 @@ process makeReport {
 // decoupling the publish from the process steps.
 process output {
     // publish inputs to output directory
-
+    label "pysam"
     publishDir "${params.out_dir}", mode: 'copy', pattern: "*"
     input:
         file fname
@@ -98,7 +98,6 @@ workflow {
         exit 1
     }
 
-
     reads = file("$params.fastq/*.fastq*", type: 'file', maxdepth: 1)
     if (reads) {
         reads = Channel.fromPath(params.fastq, type: 'dir', checkIfExists: true)

nextflow.config

@@ -12,8 +12,11 @@
 
 params {
     help = false
+    fastq = null
     out_dir = "output"
     wfversion = "v0.0.4"
+    aws_image_prefix = null
+    aws_queue = null
 }
 
 
@@ -58,6 +61,21 @@ profiles {
              cacheDir = ""
         }
     }
+
+    awsbatch {
+        process {
+            executor = 'awsbatch'
+            //queue = "${params.aws_queue}"
+            queue = "${params.aws_queue}"
+            memory = '8G'
+            withLabel:pysam {
+                container = "${params.aws_image_prefix}-wf-template:${params.wfversion}"
+            }
+            shell = ['/bin/bash', '-euo', 'pipefail']
+        }
+    }
+    aws.region = 'eu-west-1'
+    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 }